Examples
This section contains small example programs that demonstrate the use of SeqAn.
See here for instructions how to compile these examples.
Examples
See our Wiki for Basic demos. |
Basics
Computing an optimal global alignment between two sequences. | |
Computing local alignments between two sequences. | |
Examples for memory allocation. | |
Examples for common alphabets. | |
Simple iterator functions. | |
Example for some functions for handling (rooted) iterators. |
Graph
Breadth-first search through a graph. | |
Depth-first search through a graph. | |
Computing all strongly-connected-components of a graph. | |
Topological sort of a graph. | |
Computing all-pairs shortest paths. | |
Computing all-pairs shortest paths using Floyd-Warshall algorithm. | |
Hidden Markov Model code example | |
Hidden Markov Model with silent states code example | |
Ford-Fulkerson maximum flow code example | |
Kruskal's algorithm for computing a minimum spanning tree. | |
Prim's algorithm for computing a minimum spanning tree. | |
Longest increasing subsequence code example | |
Heaviest increasing subsequence code example | |
Longest common subsequence code example | |
Computing single source shortest paths using Bellman-Ford algorithm. | |
Computing single source shortest paths in a directed acyclic graph. | |
Computing single source shortest paths using Dijkstra algorithm. | |
Transitive closure code example |
Index
Example for using node predicates on a deferred suffix tree. | |
Example for using a Finder of an Index. | |
Example for using a Finder of an Index of a StringSet. | |
Example for using the MaxRepeats Iterator. | |
Example for using the Mums Iterator. | |
Simple MUMmer clone. | |
Using a Pizza & Chili Index for searching and the Pizza & Chili String for displaying. | |
Example for how to create a suffix array and use it as a dictionary. | |
Example for using the SuperMaxRepeats Iterator. |
Miscellaneous
Parsing the output of BLAST call. |
Modifier
Modifier example for reverse strings. | |
How to modify strings with a per-character functor. | |
How to combine modifiers. |
Motif Search
Examples for how to start a motif search using SeqAn's Motif Finder. |
Searching
Exact string matching. | |
Approximate string matching. | |
String matching using wildcards. |
System
Accessing sequence data in files. |
SeqAn - Sequence Analysis Library - www.seqan.de